[gmx-users] Exchange interval in REMD

[Gianluca Interlandi]

Hi Mark,

Thanks for the answer. Just to be clear: you think that a too short 
interval might introduce artefacts? I agree with this. So, do you think 
that an interval between 1 and 10 ps could be a good value?

Gianluca


On Thu, 26 Jan 2012, Mark Abraham wrote:

> On 26/01/2012 11:38 AM, Gianluca Interlandi wrote:
>> Hi,
>> 
>> I have been going through the How-to for REMD in gromacs:
>> 
>> http://www.gromacs.org/Documentation/How-tos/REMD
>> 
>> Is there a recommended value for the exchange interval and does it depend 
>> on system size? For example, is an interval of 100 ps appropriate for a 
>> sytem with 60,000 atoms? Is a too long interval simply a waste of time or 
>> can it actually introduce artefacts?
>
> There's literature by Sindhikara (sp?) and Roitberg that says you should have 
> a short an interval as possible, and other literature that says you shouldn't 
> go shorter than around the autocorrelation time of PE, ~1ps. I don't buy the 
> former, and think some of their data support the latter, and have some of my 
> own not-ready-for-publication data that I think suggests artefacts from the 
> former. Work from Hansmann et al suggests that achieving steady-state replica 
> flow is rather tricky even for seemingly trivial peptides, so increasing the 
> number of exchange attempts might help a little. I'm not aware of any good 
> case for a long interval between attempts.
>
> Mark
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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